A Brooklyn man serving time for a Queens burglary has been indicted for murdering his pregnant girlfriend in 2003 – closing a cold case that had frustrated investigators for over a decade, authorities said Friday.

Jefferson Jones, 41, was indicted after the gun he carried in the Queens burglary was found to be the same gun that used to kill Lamethia McCollum, who was nine months pregnant with his daughter, the Brooklyn District Attorney said.

McCollum was shot twice in the head and was found on the bedroom floor of her Flatlands apartment by her 8-year-old daughter, the DA said.

Jones was collared in an attempted home invasion in Queens on February 27, 2012 – and the 9 mm Glock handgun he was carrying was confirmed as the same gun that killed the pregnant McCollum, the DA said.

McCollum’s distraught mother, Lottie, told The Post in 2003 that she got a call from her young granddaughter, saying: “I don’t think my mommy is feeling very well.”

Lottie went to her daughter’s home, discovered McCollum’s body, and called 911.

“I told them that my daughter was dead on the floor,” she said.

Jones is serving 3½ years on the attempted burglary rap and was eligible for release in August 2015, said a state Department of Corrections spokeswoman.

But now he could face up to 25 years to life if convicted of killing McCollum.

“This young woman was senselessly and violently killed in the prime of her life. Now the man who is allegedly responsible for her murder must be held accountable,” said Brooklyn DA Ken Thompson, who also thanked retired NYPD detective Richard Lyman for his persistence in solving the case.